Source code for pycif.plugins.chemistries.lmdz.make_chemistry

from __future__ import annotations

from pathlib import Path

from ....utils.namelist import format_fortran_namelist
from .utils import parse_reaction




def create_chemicalscheme(self) -> None:
    reactants = []
    products = []
    products_stoi = []
    rate_type = []
    rate_terms = []
    jrates_var = []

    self.jrates_varname = []

    for reac_str in self.reactions:
        reacs, prods, stoi, rtype, rterms = parse_reaction(self, reac_str)

        reactants.append(reacs)
        products.append(prods)
        products_stoi.append(stoi)
        rate_type.append(rtype)

        if rtype == "photolysis":
            varname = rterms
            rate_terms.append([])
            jrates_var.append(varname)
            if varname not in self.jrates_varname:
                self.jrates_varname.append(varname)
        else:
            rate_terms.append(rterms)
            jrates_var.append("")

    namelists = {
        "dims": {
            "nprescr": len(self.prescribed_species),
            "nprodloss": len(self.prodloss_species),
            "ndepvel": len(self.deposition_species),
            "njrates": len(self.jrates_varname),
            "nreac": len(self.reactions),
        },
        "species": {
            "prescribed_species": self.prescribed_species,
            "prodloss_species": self.prodloss_species,
            "deposition_species": self.deposition_species,
            "jrates_varname": self.jrates_varname,
        },
        "reactions": {
            "reactants": reactants,
            "products": products,
            "products_stoi": products_stoi,
            "rate_type": rate_type,
            "rate_terms": rate_terms,
            "jrates_var": jrates_var,
        },
    }

    with open(Path(self.chem_dir, "chemical_scheme.nml"), "w") as f:
        for name, variables in namelists.items():
            f.write(format_fortran_namelist(name, variables))